LOCUS       NZ_CP117978             5636 bp    DNA     circular CON 26-MAR-2024
DEFINITION  Salmonella enterica strain B-4212 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP117978
VERSION     NZ_CP117978.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33246676
            Assembly: GCF_028743635.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5636)
  AUTHORS   Damerum,A.
  TITLE     Salmonella enterica B-4212 hifiasm Zymo Research D6300
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5636)
  AUTHORS   Damerum,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-FEB-2023) Microbiomics, Zymo Research Corporation,
            17062 Murphy Ave, Irvine, CA 92614, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Hifiasm v. 0.16.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1.0x
            Sequencing Technology             :: PacBio Sequel IIe
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_028743635.1-RS_2024_03_26
            Annotation Date                   :: 03/26/2024 02:11:10
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,746
            CDSs (total)                      :: 4,625
            Genes (coding)                    :: 4,335
            CDSs (with protein)               :: 4,335
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 290
            CDSs (without protein)            :: 290
            Pseudo Genes (ambiguous residues) :: 0 of 290
            Pseudo Genes (frameshifted)       :: 137 of 290
            Pseudo Genes (incomplete)         :: 128 of 290
            Pseudo Genes (internal stop)      :: 80 of 290
            Pseudo Genes (multiple problems)  :: 49 of 290
            Pseudo Genes (short protein)      :: 1 of 290
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117978.1.
            Bacteria and source DNA available from Annabelle Damerum, Zymo
            Research, 17062 Murphy Ave, Irvine, CA, United States, 92614.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5636
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="B-4212"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA"
                     /collection_date="2021-08-05"
     gene            complement(<1..996)
                     /gene="igaA"
                     /locus_tag="PT747_RS23695"
                     /pseudo=""
     CDS             complement(<1..996)
                     /gene="igaA"
                     /locus_tag="PT747_RS23695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_462398.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="intracellular growth attenuator protein IgaA"
                     /name="igaA"
     gene            1319..1882
                     /gene="nudE"
                     /locus_tag="PT747_RS23700"
     CDS             1319..1882
                     /gene="nudE"
                     /locus_tag="PT747_RS23700"
                     /EC_number="3.6.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000045725.1"
                     /GO_function="GO:0016787 - hydrolase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ADP compounds hydrolase NudE"
                     /protein_id="WP_000045725.1"
                     /translation="MSKSLQKPTILKVETVAQSRLFNVESVDLEFSNGVRRVYERMRPS
                     TREAVMIVPIVDEHLILIREYAVGTESYELGFSKGLIDPGETVFEAANRELKEEVGFGA
                     HNLTFLKKLSMAPSYFSSKMNIVVAEDLYPESLEGDEPEPLPQVRWPLAHLMDLLEDPD
                     FNEARNVSALFLVREWLKAQGRIA"
                     /name="nudE"
     gene            complement(1978..4530)
                     /gene="mrcA"
                     /locus_tag="PT747_RS23705"
     CDS             complement(1978..4530)
                     /gene="mrcA"
                     /locus_tag="PT747_RS23705"
                     /EC_number="2.4.1.129"
                     /EC_number="3.4.16.4"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_312265.2"
                     /GO_function="GO:0008658 - penicillin binding [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="peptidoglycan glycosyltransferase/peptidoglycan
                     DD-transpeptidase MrcA"
                     /protein_id="WP_001541017.1"
                     /translation="MKFVKYLLILAVCCILLGAGSIYGLYRYIEPQLPDVATLKDVRLQ
                     IPMQVYSADGELIAQYGEKRRIPVTLDQIPPEMINAFIATEDSRFYEHHGIDPVGIFRA
                     ASVALFSGHASQGASTITQQLARNFFLSPERTLMRKIKEAFLAIRIEQLLNKNEILELY
                     LNKIYLGYRAYGVGAAAQVYFGKTVDQLSLSEMAVIAGLPKAPSTFNPLYSMDRAIARR
                     NVVLSRMLSEGYITQAQYDQARSEPIDANYHAPEIAFSAPYLSEMVRQEMYNRYGESAY
                     EDGYRIYTTITRKVQQAAQQAVRNNVLDYDMRHGYRGPANVLWKVGETAWDSKKITDTL
                     KALPTYGPLLPAVVTSANPQEATAALADGTSVSLHMEGMRWARPYRSDTQQGPTPRKVT
                     DVVQTGQQIWVRQVDNDWWLAQVPEVNSALVSLNPQTGAVLALVGGFDFNQSKFNRATQ
                     ALRQVGSNIKPFLYTAAMDKGLTLASMLNDVPISRWDAGAGSDWRPKNSPPQYAGPIRL
                     RQGLGQSKNVVMVRAMRAMGVDYAAEYLQRFGFPAQNIVHTESLALGSASFTPMQVARG
                     YAVMANGGFLIDPYFISKIENDQGGVIFEAKPKIACPECDIPVIYGNTQKSDVLENTNV
                     EEVAVSQEQQNSAVPMPELEQANQALVAQNGTQEYAPHVINTPLAFLIKSALNTNIFGE
                     PGWMGTGWRAARDFKRRDIGGKTGTTNSSKDAWFSGYGPGVVTSVWIGFDDHRRDLGRT
                     TASGAIKDQISGYEGGAKSAQPAWDAYMKAVLEGVPEQPLTPPPGIVTVNIDRSTGQLA
                     SGGNSREEYFIEGTQPTQQAVHEVGTTIIDNGETHELF"
                     /name="mrcA"
     gene            4651..5430
                     /locus_tag="PT747_RS23710"
     CDS             4651..5430
                     /locus_tag="PT747_RS23710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_462395.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000874745.1"
                     /translation="MAFKTWQIGLHIQQHEALAIAVIRGASGWSLQRWWRLPLMNASTA
                     EGTIPDPQSLAHVLRPWSRELPLRHRIYLSFPANRTLQRAFPHPPMRLREREQVAWLSQ
                     TMARELDMDPDLLRFDFQDDALSPAFNVTAVQSKEISELLTLAQTLNVRIAAVTPDACA
                     LQRLLPFIPSGRQCLVWRDESQWLWATHYAWGRKSAREAMTLHDLAATLSVVPEHISLC
                     AEGEFDPWRAVTVRQPPVPPDGYRFAIALGLAIGEIR"
                     /name="hypothetical protein"
     gene            5430..>5636
                     /locus_tag="PT747_RS23715"
                     /pseudo=""
     CDS             5430..>5636
                     /locus_tag="PT747_RS23715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_462394.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="pilus assembly protein PilN"
                     /name="pilus assembly protein PilN"
ORIGIN
        1 aaagtttttc acttcatcat gcagggataa aaaccggccc tggcgcgcga catggcgatc
       61 aaggtaaata tcaatatccg tttgttgccc aagatcctgc gtaatgtaag gttgccagtg
      121 ggcagggtaa ataaggtcga tgatgcccag ggagatattg ttaatctgct cctgattatt
      181 ctccccaaac agtccccagc ggcggggcgt tccccgcaga cagtgaattt cccgcagcgc
      241 gcttttcgac ggcggcgcaa aaagccccca aagtccggct gccagcagca ggatagcgcc
      301 gcctatcatc cacggtacaa aaacgtctgg cgttatcaga cagaaaaaga ataacaaaaa
      361 ggaggcgacg attaacaacg cttcgcgcaa gccagccggg cggctgagcg catattcttc
      421 gtgggtctcc tgacggatat tcaacagctc aatctgctcg ctctcttcgc cgcgaatcga
      481 cgcctgcgta gaggcggtat tctgtagcgc gtagccgcgc gactcctgca tatactcttg
      541 cagcgtatgg ccgtttaaag agatcaccag cggcagcgta tccgtgagga tcagctcaac
      601 gttgttttca tcattgatgt actgttccca gaaaggcggc agatggactt cgacggagtc
      661 gaggtagtag cgccatttat taggatcgtc agtggtaatg ccgtagcggg tgatggagtg
      721 ggtcagtatc acgacactgt tgctttccgc gttcagcgtc agcgagatgg gcgcagcact
      781 ggcgcctgtc ggccccggaa cttgctggat ctggctaagg ttatcgagat agttttctac
      841 cgcgctgcgc tcttcgggca acagtttacg cgtttgcgcg tcctgaaagg cgctgatcca
      901 cggtaaactc cctcgtctgg actttacccg gaaccgccat attgccagta gagagcaggc
      961 cagcaaagca gctataaaaa tcagaatggt gctcatgctt tccccatctt actaagtctg
     1021 tcaggcgtgg tcagtcgcac cctgtccaat aaacattttt ctgtggttgg ctatcggcaa
     1081 gcgtggagtt gaacttgagc attgtaaagc gcatcccagt gaaggcaaat catagcaata
     1141 ccaccaaaaa cggaatatca gcaaattcct ggagttattt caacctattg acttttaatt
     1201 tgaaataaga attaattttt attacgttac ataaatgtaa ataaacggca attcgcattg
     1261 ccgaaaccgt gcggtatgtc gcacaatgac cacagattac actgcaaaga ttctcacaat
     1321 gagcaaatca ttacaaaaac ccaccattct gaaagtggaa accgtcgcac aatcccgact
     1381 gtttaacgta gaaagcgtgg atctggagtt cagcaacggc gtgcgtcgcg tgtatgaacg
     1441 tatgcgacca tcaacccgtg aggcggtaat gattgtgccg atcgttgatg agcatctgat
     1501 tcttattcgt gagtatgcgg tgggaaccga atcctatgag ctgggcttct cgaaaggatt
     1561 gatcgacccg ggcgagaccg tttttgaagc ggcgaaccgg gagctcaaag aagaggtcgg
     1621 gtttggcgcg cataacctga ccttcttaaa aaaactcagc atggcgccct cttatttttc
     1681 cagcaaaatg aatatcgtgg tggcggaaga tctctatccg gagtcgctgg aaggcgacga
     1741 gcctgagcca ttgccgcagg tacgctggcc gctggcgcat ttaatggatc tgctggaaga
     1801 ccccgatttt aacgaggccc gcaacgtcag cgcgctgttt ctggtacgcg agtggttgaa
     1861 agcgcagggc cgaattgcct gatggcgcgg cgttgatcaa gccaacggaa agtttgtctc
     1921 cccgttcgcc gtcatccgct aaacacaata aaaaaggcgc cggagcgcct tttttgatca
     1981 gaacagttcg tgtgtttcac cattatcaat aatggtagtt cccacctcgt gtaccgcctg
     2041 ttgtgtcggc tgcgtgcctt cgatgaaata ctcttcacgg ctattaccgc cgctcgccag
     2101 ttgtccggta ctgcggtcga tattcaccgt gacgatgccc ggcggcggcg ttagcggctg
     2161 ttccggcacg ccttccagca cggctttcat ataggcgtcc catgcaggtt gcgcgctctt
     2221 cgcgccgccc tcatagccgg agatttgatc tttgatcgcg ccggaagcgg tggtgcggcc
     2281 taaatcacgg cggtgatcgt caaagccgat ccatacggaa gtgacgacgc caggaccata
     2341 gccagagaac catgcgtctt tcgagctgtt ggtcgtaccg gttttgccgc cgatatcgcg
     2401 acgtttaaaa tcgcgcgccg cacgccagcc ggtacccatc cagccgggtt cgccgaagat
     2461 attggtgttc agcgcgcttt taatcagaaa cgccagcggc gtattgatca catgcggcgc
     2521 gtactcctgc gtgccgtttt gcgcgaccag cgcctggttt gcctgttcca gctcaggcat
     2581 cggtacggcg ctgttttgct gctcttgcga aaccgcgacc tcttccacat tggtgttttc
     2641 cagcacgtcg gatttctgcg tattgccgta aatgaccggg atatcgcact ccgggcaggc
     2701 gattttcggt ttcgcttcga agatcacgcc gccctgatcg ttctcaatct tgctgatgaa
     2761 atacgggtcg atcaggaaac cgccgttcgc catcaccgca taaccgcgcg caacctgcat
     2821 cggcgtgaag gaggcggagc ccagcgccag cgattcggta tgcacgatat tctgcgccgg
     2881 gaagccgaag cgttgcagat actccgccgc atagtcgacg cccatggcgc gcatggcgcg
     2941 taccatcacc acgtttttcg actgccccag cccctggcgt aaacgaatcg gtccggcgta
     3001 ctgcggcgga gagtttttcg gacgccagtc tgaacctgcc ccggcgtccc agcgggaaat
     3061 cggcacatcg ttgagcatac tggcgagcgt caggccttta tccattgcgg cggtgtagag
     3121 gaacggtttg atgttcgacc ccacctgacg caaagcttgc gtcgcgcggt taaatttact
     3181 ctgattaaaa tcgaaaccgc cgaccagcgc cagtaccgcg ccagtttgcg ggttaagcga
     3241 aaccagcgcg gagttcactt ccggtacctg cgccagccac cagtcgttat ccacctgacg
     3301 aacccagatt tgctgacctg tctggacgac atcggtaact ttacgcggcg tcggcccctg
     3361 ctgtgtatcc gagcggtaag gtcgcgccca acgcattcct tccatatgta gcgaaacgga
     3421 cgtaccgtcg gcaagcgcag cggtcgcctc ttgcggatta gcgctggtga ccacggcggg
     3481 aagcagcggt ccgtaggtcg gcaacgcttt caacgtatcg gtaatttttt tactgtccca
     3541 cgctgtttcg cccactttcc atagcacatt cgccgggccg cgataaccgt ggcgcatgtc
     3601 atagtccagc acgttattac gcaccgcctg ttgcgcggcc tgctgcactt tgcgggtgat
     3661 ggtcgtgtaa atacgataac catcttcgta agcgctttcg ccataacggt tatacatttc
     3721 ctggcgcacc atttccgaca gataaggtgc ggagaaggcg atttccggcg cgtgataatt
     3781 tgcgtcgata ggttcgctac gggcctgatc gtactgcgcc tgagtgatat atccctcgct
     3841 taacattcgc gagagcacta cgttacggcg cgctatcgcc cgatccatcg agtagagcgg
     3901 gttaaaggta gaaggcgctt taggtagccc ggcgataacc gccatttcgc ttaaactaag
     3961 ctggtcgacc gtcttaccaa agtagacctg tgccgccgcg ccaacgccat aggcgcggta
     4021 gccgagatag atcttgttca gatagagttc gaggatctca tttttattca gcaactgctc
     4081 aatacgaatc gccagaaacg cttccttgat cttgcgcatt agcgtgcgtt cggggctaag
     4141 gaagaagttt cgcgccagtt gctgggtaat ggtacttgct ccctgcgatg cgtgaccgga
     4201 gaagagcgcg acgctggccg cacggaaaat acctaccggg tcaatgccgt gatgctcata
     4261 aaagcggcta tcttcggtgg cgataaaggc gttgatcatt tccggcggaa tttgatcgag
     4321 cgtaacggga atacggcgtt tttcgccata ttgcgcgata agttcgccat ccgcgctgta
     4381 aacctgcatc ggaatttgca aacgcacatc tttcaatgtc gcgacgtcag gtagctgcgg
     4441 ctcaatatag cgataaaggc cataaatcga gcctgctccc agcaggatgc aacatactgc
     4501 aaggatcaat aaatacttta cgaacttcac tggagatttc ccatttagtg tcatttgggc
     4561 agtttataaa caaacgcgcg gtagtataaa ggcaagccag acgcattgat atacccgtta
     4621 acgcgacggg tgataaggag atcgaccgtt atggctttta aaacctggca aataggattg
     4681 catattcagc agcatgaagc gctggccatc gccgttattc gcggcgcatc gggctggtcc
     4741 ctgcaacgtt ggtggcgact gccgctaatg aacgcctcca cggcagaggg tacgattcct
     4801 gacccgcaat cgctggctca cgtactgcga ccctggagcc gcgagctgcc gctacgtcac
     4861 cgtatttatc tctcttttcc cgcaaatcgg acattgcaac gcgcttttcc acatccgccg
     4921 atgcgtctgc gggaacgtga gcaagtcgca tggctttcac aaacgatggc gcgtgagctg
     4981 gatatggatc cggacttatt gcgtttcgac tttcaggacg atgcgctaag ccccgcgttc
     5041 aacgttaccg ccgtgcaaag caaagaaatt tcagagctgt taacgctggc gcaaacgctc
     5101 aatgtgcgca tcgctgctgt aacgcccgat gcctgcgcgc tacagcgctt gctgccgttt
     5161 ataccttcgg ggcggcaatg tctggtctgg cgcgatgaga gccagtggct gtgggcgacg
     5221 cactatgcgt gggggcgtaa atcggcgcga gaggcgatga cgctgcatga ccttgccgca
     5281 acattatccg tcgtgccgga acatatttca ttatgcgccg aaggcgaatt cgacccctgg
     5341 cgcgccgtaa ccgtccgcca accgccggtt ccgccggacg gttatcgctt tgcgattgcg
     5401 ctggggttag ccatagggga gatacgctga tggcgcattc tgtcaatttg ctcccctggc
     5461 ggcgccaaca ttacgtagcg cgtctgcggc tgtggtgcgt ggtatggggc gcgtccctgc
     5521 tgctgatagc aagcctcgcg acgatcgccc ggttggtttt ttggcaggag gggaggatta
     5581 acgagctgct actgacggcg gaaaacggac acacgacggc gcttgcggcg aacata
//
